Motile cilia are structures that line the inner walls of several organs, including the brain. By beating in metachronal patterns, motile cilia mediate cerebrospinal fluid flow, serving a regulatory role in the brain during neural development [1, 2]. The underlying mechanisms of this flow and the resulting transport in brain ventricles is not yet fully understood. In this work, we analyze the flow and transport in brain ventricles from a Lagrangian perspective. We use a finite element model calibrated with experimental data to simulate flow fields. With these flow fields, we calculate particle trajectories and from these derive finite-time Lyapunov exponent fields, which serve as an approximation to Lagrangian coherent structures of the flow [3]. These structures provide insights on the governing structures of advective transport in the ventricles. We study both flow fields corresponding to healthy brains, as well as flow fields simulating brains suffering from neuropathologies that lead to deficiencies in ciliary movement. The goal is to increase our knowledge of how the pathologies alter the flow and transport in brain ventricles, and how this affects brain function.